High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid

Abstract

Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function remain largely unknown. The decoration protein pb10 of phage T5 binds at the centre of the 120 hexamers formed by the major capsid protein. Here we determined the 3D structure of pb10 and investigated its capsid-binding properties using NMR, SAXS, cryoEM and SPR. Pb10 consists of an α-helical capsid-binding domain and an Ig-like domain exposed to the solvent. It binds to the T5 capsid with a remarkably high affinity and its binding kinetics is characterized by a very slow dissociation rate. We propose that the conformational exchange events observed in the capsid-binding domain enable rearrangements upon binding that contribute to the quasi-irreversibility of the pb10-capsid interaction. Moreover we show that pb10 binding is a highly cooperative process, which favours immediate rebinding of newly dissociated pb10 to the 120 hexamers of the capsid protein. In extreme conditions, pb10 protects the phage from releasing its genome. We conclude that pb10 may function to reinforce the capsid thus favouring phage survival in harsh environments.

Shigella Phages Isolated during a Dysentery Outbreak Reveal Uncommon Structures and Broad Species Diversity

“…4C), giving the capsid a maximum diameter of 786 Å. Decoration proteins have been characterized for some bacteriophages, and most of these proteins contain at least one immunoglobulin (Ig)-like domain (34,35), with the exception of the Dec protein of phage L, which is formed primarily by ␤-sheets (36). Using a tBLASTn sequence alignment against all known decoration proteins, phages Sf13 through Sf19 were found to contain gene products with significant similarity to T5 pb10 (35). This protein is composed of an ␣-helical capsid-binding domain at the N terminus and a single C-terminal Ig-like domain.…”

“…Structurally, the location of this decoration protein on the capsid surface is also unlike those of previously described proteins. The decoration protein of N4 binds along the edges of each hexamer (34), whereas those of T4, RB49, and T5 bind at the center of each hexamer (35,37,38). The phage L decoration protein is more complex, binding preferentially to the quasi-3-fold but not the true 3-fold sites (36,39).…”

The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy

“…For dsDNA tailed phages and related viruses, decoration proteins can occupy the capsid lattice in several different positions. Some decoration proteins bind capsids at the center of hexamers including those of phages T4, T5, RB49, and Sf13 through Sf19, [63–66]. Other decoration proteins bind the edges of hexamers as exemplified by gp17 in phage N4 [67].…”

“…Indeed there is a wide range of reported K D s for various decoration proteins. Phage L’s Dec and T4’s Hoc bind their respective capsids with nM affinity, whereas pb10 binds phage T5 with pM affinity [36,63,73]. Taken together, variations in binding affinities and saturating versus discriminating binding behavior suggests that decoration proteins are capable of recognizing subtle differences in capsid lattices.…”

“…In dsDNA-containing tailed phages, previously studied decoration proteins for which atomic-resolution structures are known have two basic types of protein folds. Decoration proteins such as phage T5’s pb10 and T4’s hoc, have an overall Ig domain fold [63,66]. A second, more common type of decoration protein, exemplified by phage lambda’s gpD, P74-26’s gp87, phage 21’s SHP, and TW1 gp56, have similar polypeptide folds and form a symmetric trimer with an N-terminal β-tulip domain and an α/β subdomain that binds and stabilizes capsids through hydrophobic interfaces [70,76].…”